{"id":"W2942158514","doi":"10.1038/s41598-019-42978-1","title":"Environmental DNA metabarcoding to detect pathogenic Leptospira and associated organisms in leptospirosis-endemic areas of Japan","year":2019,"lang":"en","type":"article","venue":"Scientific Reports","topic":"Leptospirosis research and findings","field":"Immunology and Microbiology","cited_by":56,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"Institute of Genetics; Japan Society for the Promotion of Science; University of the Ryukyus; Ministry of Education, Culture, Sports, Science and Technology","keywords":"Leptospira; Leptospirosis; Biology; Environmental DNA; Amplicon; Amplicon sequencing; Microbiome; Leptospira interrogans; Abiotic component; DNA sequencing; Zoonosis; Zoology; Polymerase chain reaction; Ecology; Biodiversity; Genetics; DNA; Bacteria; 16S ribosomal RNA; Virology; Gene","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":["insufficient_payload"],"consensus_categories":[],"category_scores_codex":[0.001848696,0.0002217755,0.0004622965,0.0004175887,0.0001927045,0.0000722165,0.0002298518,0.0002346651,0.001109784],"category_scores_gemma":[0.0003282357,0.0002051225,0.0001203521,0.000527825,0.0003582631,0.000195802,0.0003202613,0.0003284993,0.0003323207],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000151251,"about_ca_system_score_gemma":0.0001170671,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00005670755,"about_ca_topic_score_gemma":0.00004008708,"domain_scores_codex":[0.9973709,0.000144236,0.0006709602,0.0009230506,0.0002057674,0.0006850989],"domain_scores_gemma":[0.9989044,0.00006761387,0.0003048351,0.0005899888,0.00003708273,0.00009608428],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.00001627371,0.00005969812,0.2975245,0.000009616597,0.00003793882,0.00001045397,0.0004321329,0.000001884169,0.6993567,0.0000119804,0.0002678432,0.002271038],"study_design_scores_gemma":[0.0006046572,0.0002056298,0.2859578,0.00005821379,0.00002148511,0.00008719205,0.0003643446,0.000002241237,0.7073404,0.000355818,0.004752509,0.0002497619],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9968096,0.0006867332,0.00001002514,0.00005956689,0.00139802,0.0006148494,0.000023632,0.00003517491,0.0003624108],"genre_scores_gemma":[0.9969193,0.0000160756,0.00005850121,0.00003613416,0.000007981705,0.00002327407,0.00009022969,0.00002438094,0.002824149],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.01156668,"threshold_uncertainty_score":0.9998034,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.009093314308969409,"score_gpt":0.2182062019828592,"score_spread":0.2091128876738898,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}